guppy_basecaller: env/lib/python3.7/site-packages/cwltool/schemas/v1.1.0-dev1/CommandLineTool.yml annotate

author	shellac
date	Sat, 02 May 2020 07:14:21 -0400
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children

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0 26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	1 saladVersion: v1.1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	2 $base: "https://w3id.org/cwl/cwl#"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	3
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	4 $namespaces:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	5 cwl: "https://w3id.org/cwl/cwl#"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	6
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	7 $graph:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	8
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	9 - name: CommandLineToolDoc
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	10 type: documentation
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	11 doc:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	12 - \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	13 # Common Workflow Language (CWL) Command Line Tool Description, v1.1.0-dev1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	14
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	15 This version:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	16 * https://w3id.org/cwl/v1.1.0-dev1/
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	17
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	18 Current version:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	19 * https://w3id.org/cwl/
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	20 - "\n\n"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	21 - {$include: contrib.md}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	22 - "\n\n"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	23 - \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	24 # Abstract
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	25
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	26 A Command Line Tool is a non-interactive executable program that reads
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	27 some input, performs a computation, and terminates after producing some
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	28 output. Command line programs are a flexible unit of code sharing and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	29 reuse, unfortunately the syntax and input/output semantics among command
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	30 line programs is extremely heterogeneous. A common layer for describing
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	31 the syntax and semantics of programs can reduce this incidental
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	32 complexity by providing a consistent way to connect programs together.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	33 This specification defines the Common Workflow Language (CWL) Command
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	34 Line Tool Description, a vendor-neutral standard for describing the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	35 syntax and input/output semantics of command line programs.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	36
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	37 - {$include: intro.md}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	38
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	39 - \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	40 ## Introduction to the CWL Command Line Tool standard v1.1.0-dev1
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	41
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	42 This specification represents the latest development release from the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	43 CWL group. Since the v1.0 release, v1.1 introduces the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	44 following updates to the CWL Command Line Tool standard.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	45 Documents should use `cwlVersion: v1.1.0-dev1` to make use of new
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	46 syntax and features introduced in v1.1.0-dev1. Existing v1.0 documents
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	47 should be trivially updatable by changing `cwlVersion`, however
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	48 CWL documents that relied on previously undefined or
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	49 underspecified behavior may have slightly different behavior in
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	50 v1.1.0-dev1.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	51
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	52 ## Changelog
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	53
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	54 * Clarify behavior around `ENTRYPOINT` and `CMD` in containers.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	55 * Clarify documentation around `valueFrom` and `null` inputs.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	56 * Default values for some fields are now expressed in the schema.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	57 * When defining record types with `CommandInputRecordSchema`, fields of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	58 type `File` may now include `format`, `loadContents`,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	59 `secondaryFiles` and `streamable`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	60 * `CommandInputRecordSchema`, `CommandOutputRecordSchema`,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	61 `CommandInputEnumSchema and `CommandInputArraySchema` now have an optional
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	62 `doc` field.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	63 * `inputBinding` has been added as an optional field for
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	64 `CommandInputRecordSchema` (was previously in CWL `draft-3` but
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	65 disappeared in `v1.0`).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	66 * Any `doc` field may be an array of strings in addition to the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	67 previously allowed single string.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	68 * Addition of `stdin` type shortcut for
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	69 [`CommandInputParameter`](#CommandInputParameter).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	70 * Clarify that the designated output directory should be empty
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	71 except for files or directories specified using
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	72 [InitialWorkDirRequirement](#InitialWorkDirRequirement).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	73 * Clarify semantics of `shellQuote`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	74 * Expressions are now allowed to evaluate to `null` or `Dirent` in
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	75 [InitialWorkDirRequirement.listing](#InitialWorkDirRequirement).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	76 * Items in [InitialWorkDirRequirement.listing](#InitialWorkDirRequirement)
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	77 are now allowed to be `null` and `array<File \| Directory>`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	78 * Clarify behavior of secondaryFiles on output.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	79 * [Addition](#Requirements_and_hints) of `cwl:requirements` field to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	80 input object documents.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	81 * Clarify behavior of `glob` for absolute paths and symlinks.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	82 * Clarify behavior of `glob` to include directories.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	83 * `secondaryFiles` can now be explicitly marked as `required` or not.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	84 * Clarify `CommandLineTool.arguments` documentation.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	85 * Clarify that `runtime.outdir` and `runtime.tmpdir` must be distinct
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	86 directories.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	87 * Clarify that unspecified details related to execution are left open to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	88 the platform.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	89 * Added `InputParameter.loadContents` field. Use of `loadContents` in
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	90 `InputBinding` is deprecated; it is preserved for v1.0 backwards
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	91 compatability and will be removed in CWL v2.0.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	92 * [Added](#ToolTimeLimit) `ToolTimeLimit` feature, allows setting
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	93 an upper limit on the execution time of a CommandLineTool.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	94 * [Added](#WorkReuse) `WorkReuse` feature, allowing to enable or disable the reuse
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	95 behavior for a particular tool or step for implementations that
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	96 support reusing output from past work.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	97 * [Added](#NetworkAccess) `NetworkAccess` feature, allowing to indicate whether a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	98 process requires outgoing network access.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	99 * [Added](#InplaceUpdateRequirement) `InplaceUpdateRequirement` feature, allowing tools to directly
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	100 update files with `writable: true` in `InitialWorkDirRequirement`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	101 * [Added](#LoadListingRequirement) `LoadListingRequirement`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	102 and [loadListing](#LoadContents) to control whether and how
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	103 `Directory` listings should be loaded for use in expressions.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	104 * The position field of the [CommandLineBinding](#CommandLineBinding) can
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	105 now be calculated from a CWL Expression.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	106 * The exit code of a CommandLineTool invocation is now
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	107 available to expressions in `outputEval` as `runtime.exitCode`
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	108 * [Better explain](#map) the `map<…>` notation that has existed since v1.0.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	109 * Fixed schema error where the `type` field inside the `inputs` and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	110 `outputs` field was incorrectly listed as optional.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	111 * For multi-Process CWL documents, if no particular process is named then
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	112 the process with the `id` of `#main` is chosen.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	113
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	114 See also the [CWL Workflow Description, v1.1.0-dev1 changelog](Workflow.html#Changelog).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	115
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	116 ## Purpose
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	117
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	118 Standalone programs are a flexible and interoperable form of code reuse.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	119 Unlike monolithic applications, applications and analysis workflows which
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	120 are composed of multiple separate programs can be written in multiple
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	121 languages and execute concurrently on multiple hosts. However, POSIX
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	122 does not dictate computer-readable grammar or semantics for program input
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	123 and output, resulting in extremely heterogeneous command line grammar and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	124 input/output semantics among program. This is a particular problem in
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	125 distributed computing (multi-node compute clusters) and virtualized
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	126 environments (such as Docker containers) where it is often necessary to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	127 provision resources such as input files before executing the program.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	128
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	129 Often this gap is filled by hard coding program invocation and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	130 implicitly assuming requirements will be met, or abstracting program
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	131 invocation with wrapper scripts or descriptor documents. Unfortunately,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	132 where these approaches are application or platform specific it creates a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	133 significant barrier to reproducibility and portability, as methods
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	134 developed for one platform must be manually ported to be used on new
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	135 platforms. Similarly it creates redundant work, as wrappers for popular
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	136 tools must be rewritten for each application or platform in use.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	137
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	138 The Common Workflow Language Command Line Tool Description is designed to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	139 provide a common standard description of grammar and semantics for
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	140 invoking programs used in data-intensive fields such as Bioinformatics,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	141 Chemistry, Physics, Astronomy, and Statistics. This specification
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	142 attempts to define a precise data and execution model for Command Line Tools that
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	143 can be implemented on a variety of computing platforms, ranging from a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	144 single workstation to cluster, grid, cloud, and high performance
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	145 computing platforms. Details related to execution of these programs not
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	146 laid out in this specification are open to interpretation by the computing
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	147 platform implementing this specification.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	148
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	149 - {$include: concepts.md}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	150 - {$include: invocation.md}
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	151
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	152
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	153 - type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	154 name: EnvironmentDef
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	155 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	156 Define an environment variable that will be set in the runtime environment
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	157 by the workflow platform when executing the command line tool. May be the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	158 result of executing an expression, such as getting a parameter from input.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	159 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	160 - name: envName
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	161 type: string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	162 doc: The environment variable name
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	163 - name: envValue
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	164 type: [string, Expression]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	165 doc: The environment variable value
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	166
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	167 - type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	168 name: CommandLineBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	169 extends: InputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	170 docParent: "#CommandInputParameter"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	171 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	172
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	173 When listed under `inputBinding` in the input schema, the term
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	174 "value" refers to the the corresponding value in the input object. For
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	175 binding objects listed in `CommandLineTool.arguments`, the term "value"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	176 refers to the effective value after evaluating `valueFrom`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	177
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	178 The binding behavior when building the command line depends on the data
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	179 type of the value. If there is a mismatch between the type described by
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	180 the input schema and the effective value, such as resulting from an
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	181 expression evaluation, an implementation must use the data type of the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	182 effective value.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	183
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	184 - string: Add `prefix` and the string to the command line.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	185
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	186 - number: Add `prefix` and decimal representation to command line.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	187
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	188 - boolean: If true, add `prefix` to the command line. If false, add
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	189 nothing.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	190
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	191 - File: Add `prefix` and the value of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	192 [`File.path`](#File) to the command line.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	193
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	194 - Directory: Add `prefix` and the value of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	195 [`Directory.path`](#Directory) to the command line.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	196
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	197 - array: If `itemSeparator` is specified, add `prefix` and the join
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	198 the array into a single string with `itemSeparator` separating the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	199 items. Otherwise first add `prefix`, then recursively process
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	200 individual elements.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	201 If the array is empty, it does not add anything to command line.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	202
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	203 - object: Add `prefix` only, and recursively add object fields for
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	204 which `inputBinding` is specified.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	205
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	206 - null: Add nothing.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	207
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	208 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	209 - name: position
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	210 type: [ int, Expression, string, "null" ]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	211 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	212 The sorting key. Default position is 0. If the inputBinding is
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	213 associated with an input parameter, then the value of `self` in the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	214 expression will be the value of the input parameter. Input parameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	215 defaults (as specified by the `InputParameter.default` field) must be
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	216 applied before evaluating the expression. Expressions must return a
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	217 single value of type int or a null.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	218 - name: prefix
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	219 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	220 doc: "Command line prefix to add before the value."
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	221 - name: separate
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	222 type: boolean?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	223 default: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	224 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	225 If true (default), then the prefix and value must be added as separate
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	226 command line arguments; if false, prefix and value must be concatenated
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	227 into a single command line argument.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	228 - name: itemSeparator
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	229 type: string?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	230 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	231 Join the array elements into a single string with the elements
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	232 separated by by `itemSeparator`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	233 - name: valueFrom
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	234 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	235 - "null"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	236 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	237 - Expression
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	238 jsonldPredicate: "cwl:valueFrom"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	239 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	240 If `valueFrom` is a constant string value, use this as the value and
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	241 apply the binding rules above.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	242
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	243 If `valueFrom` is an expression, evaluate the expression to yield the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	244 actual value to use to build the command line and apply the binding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	245 rules above. If the inputBinding is associated with an input
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	246 parameter, the value of `self` in the expression will be the value of
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	247 the input parameter. Input parameter defaults (as specified by the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	248 `InputParameter.default` field) must be applied before evaluating the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	249 expression.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	250
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	251 If the value of the associated input parameter is `null`, `valueFrom` is
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	252 not evaluated and nothing is added to the command line.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	253
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	254 When a binding is part of the `CommandLineTool.arguments` field,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	255 the `valueFrom` field is required.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	256
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	257 - name: shellQuote
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	258 type: boolean?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	259 default: true
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	260 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	261 If `ShellCommandRequirement` is in the requirements for the current command,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	262 this controls whether the value is quoted on the command line (default is true).
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	263 Use `shellQuote: false` to inject metacharacters for operations such as pipes.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	264
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	265 If `shellQuote` is true or not provided, the implementation must not
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	266 permit interpretation of any shell metacharacters or directives.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	267
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	268
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	269 - type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	270 name: CommandOutputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	271 extends: LoadContents
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	272 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	273 Describes how to generate an output parameter based on the files produced
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	274 by a CommandLineTool.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	275
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	276 The output parameter value is generated by applying these operations in the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	277 following order:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	278
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	279 - glob
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	280 - loadContents
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	281 - outputEval
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	282 - secondaryFiles
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	283 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	284 - name: glob
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	285 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	286 - "null"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	287 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	288 - Expression
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	289 - type: array
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	290 items: string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	291 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	292 Find files or directories relative to the output directory, using POSIX
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	293 glob(3) pathname matching. If an array is provided, find files or
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	294 directories that match any pattern in the array. If an expression is
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	295 provided, the expression must return a string or an array of strings,
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	296 which will then be evaluated as one or more glob patterns. Must only
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	297 match and return files/directories which actually exist.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	298
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	299 If the value of glob is a relative path pattern (does not
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	300 begin with a slash '/') then it is resolved relative to the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	301 output directory. If the value of the glob is an absolute
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	302 path pattern (it does begin with a slash '/') then it must
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	303 refer to a path within the output directory. It is an error
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	304 if any glob resolves to a path outside the output directory.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	305 Specifically this means globs with relative paths containing
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	306 '..' or absolute paths that refer outside the output directory
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	307 are illegal.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	308
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	309 A glob may match a path within the output directory which is
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	310 actually a symlink to another file. In this case, the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	311 expected behavior is for the resulting File/Directory object to take the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	312 `basename` (and corresponding `nameroot` and `nameext`) of the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	313 symlink. The `location` of the File/Directory is implementation
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	314 dependent, but logically the File/Directory should have the same content
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	315 as the symlink target. Platforms may stage output files/directories to
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	316 cloud storage that lack the concept of a symlink. In
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	317 this case file content and directories may be duplicated, or (to avoid
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	318 duplication) the File/Directory `location` may refer to the symlink
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	319 target.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	320
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	321 It is an error if a symlink in the output directory (or any
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	322 symlink in a chain of links) refers to any file or directory
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	323 that is not under an input or output directory.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	324
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	325 Implementations may shut down a container before globbing
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	326 output, so globs and expressions must not assume access to the
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	327 container filesystem except for declared input and output.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	328
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	329 - name: outputEval
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	330 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	331 - "null"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	332 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	333 - Expression
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	334 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	335 Evaluate an expression to generate the output value. If
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	336 `glob` was specified, the value of `self` must be an array
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	337 containing file objects that were matched. If no files were
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	338 matched, `self` must be a zero length array; if a single file
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	339 was matched, the value of `self` is an array of a single
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	340 element. Additionally, if `loadContents` is `true`, the File
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	341 objects must include up to the first 64 KiB of file contents
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	342 in the `contents` field. The exit code of the process is
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	343 available in the expression as `runtime.exitCode`.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	344
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	345 - name: CommandLineBindable
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	346 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	347 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	348 inputBinding:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	349 type: CommandLineBinding?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	350 jsonldPredicate: "cwl:inputBinding"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	351 doc: Describes how to turn this object into command line arguments.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	352
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	353 - name: CommandInputRecordField
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	354 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	355 extends: [InputRecordField, CommandLineBindable]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	356 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	357 - specializeFrom: InputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	358 specializeTo: CommandInputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	359 - specializeFrom: InputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	360 specializeTo: CommandInputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	361 - specializeFrom: InputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	362 specializeTo: CommandInputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	363 - specializeFrom: InputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	364 specializeTo: CommandLineBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	365
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	366
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	367 - name: CommandInputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	368 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	369 extends: [InputRecordSchema, CommandInputSchema, CommandLineBindable]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	370 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	371 - specializeFrom: InputRecordField
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	372 specializeTo: CommandInputRecordField
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	373 - specializeFrom: InputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	374 specializeTo: CommandLineBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	375
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	376
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	377 - name: CommandInputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	378 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	379 extends: [InputEnumSchema, CommandInputSchema, CommandLineBindable]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	380 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	381 - specializeFrom: InputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	382 specializeTo: CommandLineBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	383
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	384
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	385 - name: CommandInputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	386 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	387 extends: [InputArraySchema, CommandInputSchema, CommandLineBindable]
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	388 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	389 - specializeFrom: InputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	390 specializeTo: CommandInputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	391 - specializeFrom: InputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	392 specializeTo: CommandInputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	393 - specializeFrom: InputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	394 specializeTo: CommandInputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	395 - specializeFrom: InputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	396 specializeTo: CommandLineBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	397
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	398
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	399 - name: CommandOutputRecordField
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	400 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	401 extends: OutputRecordField
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	402 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	403 - specializeFrom: OutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	404 specializeTo: CommandOutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	405 - specializeFrom: OutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	406 specializeTo: CommandOutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	407 - specializeFrom: OutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	408 specializeTo: CommandOutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	409 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	410 - name: outputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	411 type: CommandOutputBinding?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	412 jsonldPredicate: "cwl:outputBinding"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	413 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	414 Describes how to generate this output object based on the files
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	415 produced by a CommandLineTool
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	416
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	417
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	418 - name: CommandOutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	419 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	420 extends: OutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	421 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	422 - specializeFrom: OutputRecordField
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	423 specializeTo: CommandOutputRecordField
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	424
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	425
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	426 - name: CommandOutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	427 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	428 extends: OutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	429 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	430 - specializeFrom: OutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	431 specializeTo: CommandOutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	432 - specializeFrom: OutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	433 specializeTo: CommandOutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	434 - specializeFrom: OutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	435 specializeTo: CommandOutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	436
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	437
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	438 - name: CommandOutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	439 type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	440 extends: OutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	441 specialize:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	442 - specializeFrom: OutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	443 specializeTo: CommandOutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	444 - specializeFrom: OutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	445 specializeTo: CommandOutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	446 - specializeFrom: OutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	447 specializeTo: CommandOutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	448
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	449
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	450 - type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	451 name: CommandInputParameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	452 extends: InputParameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	453 doc: An input parameter for a CommandLineTool.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	454 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	455 - name: type
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	456 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	457 - CWLType
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	458 - stdin
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	459 - CommandInputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	460 - CommandInputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	461 - CommandInputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	462 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	463 - type: array
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	464 items:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	465 - CWLType
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	466 - CommandInputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	467 - CommandInputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	468 - CommandInputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	469 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	470 jsonldPredicate:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	471 "_id": "sld:type"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	472 "_type": "@vocab"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	473 refScope: 2
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	474 typeDSL: True
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	475 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	476 Specify valid types of data that may be assigned to this parameter.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	477 - name: inputBinding
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	478 type: CommandLineBinding?
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	479 doc: \|
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	480 Describes how to turns the input parameters of a process into
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	481 command line arguments.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	482 jsonldPredicate: "cwl:inputBinding"
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	483
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	484 - type: record
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	485 name: CommandOutputParameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	486 extends: OutputParameter
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	487 doc: An output parameter for a CommandLineTool.
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	488 fields:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	489 - name: type
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	490 type:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	491 - CWLType
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	492 - stdout
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	493 - stderr
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	494 - CommandOutputRecordSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	495 - CommandOutputEnumSchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	496 - CommandOutputArraySchema
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	497 - string
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	498 - type: array
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	499 items:
26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783" shellac parents: diff changeset	500 - CWLType

0

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1 saladVersion: v1.1

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2 $base: "https://w3id.org/cwl/cwl#"

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3

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4 $namespaces:

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5 cwl: "https://w3id.org/cwl/cwl#"

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6

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7 $graph:

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8

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9 - name: CommandLineToolDoc

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10 type: documentation

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11 doc:

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12 - |

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13 # Common Workflow Language (CWL) Command Line Tool Description, v1.1.0-dev1

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14

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15 This version:

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16 * https://w3id.org/cwl/v1.1.0-dev1/

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17

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18 Current version:

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19 * https://w3id.org/cwl/

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20 - "\n\n"

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21 - {$include: contrib.md}

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22 - "\n\n"

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23 - |

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24 # Abstract

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25

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26 A Command Line Tool is a non-interactive executable program that reads

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27 some input, performs a computation, and terminates after producing some

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28 output. Command line programs are a flexible unit of code sharing and

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29 reuse, unfortunately the syntax and input/output semantics among command

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30 line programs is extremely heterogeneous. A common layer for describing

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31 the syntax and semantics of programs can reduce this incidental

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32 complexity by providing a consistent way to connect programs together.

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33 This specification defines the Common Workflow Language (CWL) Command

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34 Line Tool Description, a vendor-neutral standard for describing the

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35 syntax and input/output semantics of command line programs.

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36

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37 - {$include: intro.md}

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38

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39 - |

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40 ## Introduction to the CWL Command Line Tool standard v1.1.0-dev1

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41

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42 This specification represents the latest development release from the

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43 CWL group. Since the v1.0 release, v1.1 introduces the

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44 following updates to the CWL Command Line Tool standard.

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45 Documents should use `cwlVersion: v1.1.0-dev1` to make use of new

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46 syntax and features introduced in v1.1.0-dev1. Existing v1.0 documents

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47 should be trivially updatable by changing `cwlVersion`, however

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48 CWL documents that relied on previously undefined or

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49 underspecified behavior may have slightly different behavior in

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50 v1.1.0-dev1.

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51

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52 ## Changelog

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53

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54 * Clarify behavior around `ENTRYPOINT` and `CMD` in containers.

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55 * Clarify documentation around `valueFrom` and `null` inputs.

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56 * Default values for some fields are now expressed in the schema.

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57 * When defining record types with `CommandInputRecordSchema`, fields of

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58 type `File` may now include `format`, `loadContents`,

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59 `secondaryFiles` and `streamable`.

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60 * `CommandInputRecordSchema`, `CommandOutputRecordSchema`,

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61 `CommandInputEnumSchema and `CommandInputArraySchema` now have an optional

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62 `doc` field.

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63 * `inputBinding` has been added as an optional field for

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64 `CommandInputRecordSchema` (was previously in CWL `draft-3` but

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65 disappeared in `v1.0`).

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66 * Any `doc` field may be an array of strings in addition to the

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67 previously allowed single string.

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68 * Addition of `stdin` type shortcut for

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69 [`CommandInputParameter`](#CommandInputParameter).

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70 * Clarify that the designated output directory should be empty

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71 except for files or directories specified using

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72 [InitialWorkDirRequirement](#InitialWorkDirRequirement).

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73 * Clarify semantics of `shellQuote`.

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74 * Expressions are now allowed to evaluate to `null` or `Dirent` in

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75 [InitialWorkDirRequirement.listing](#InitialWorkDirRequirement).

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76 * Items in [InitialWorkDirRequirement.listing](#InitialWorkDirRequirement)

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77 are now allowed to be `null` and `array<File | Directory>`.

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78 * Clarify behavior of secondaryFiles on output.

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79 * [Addition](#Requirements_and_hints) of `cwl:requirements` field to

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80 input object documents.

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81 * Clarify behavior of `glob` for absolute paths and symlinks.

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82 * Clarify behavior of `glob` to include directories.

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83 * `secondaryFiles` can now be explicitly marked as `required` or not.

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84 * Clarify `CommandLineTool.arguments` documentation.

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85 * Clarify that `runtime.outdir` and `runtime.tmpdir` must be distinct

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86 directories.

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87 * Clarify that unspecified details related to execution are left open to

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88 the platform.

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89 * Added `InputParameter.loadContents` field. Use of `loadContents` in

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90 `InputBinding` is deprecated; it is preserved for v1.0 backwards

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91 compatability and will be removed in CWL v2.0.

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92 * [Added](#ToolTimeLimit) `ToolTimeLimit` feature, allows setting

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93 an upper limit on the execution time of a CommandLineTool.

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94 * [Added](#WorkReuse) `WorkReuse` feature, allowing to enable or disable the reuse

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95 behavior for a particular tool or step for implementations that

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96 support reusing output from past work.

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97 * [Added](#NetworkAccess) `NetworkAccess` feature, allowing to indicate whether a

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98 process requires outgoing network access.

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99 * [Added](#InplaceUpdateRequirement) `InplaceUpdateRequirement` feature, allowing tools to directly

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100 update files with `writable: true` in `InitialWorkDirRequirement`.

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101 * [Added](#LoadListingRequirement) `LoadListingRequirement`

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102 and [loadListing](#LoadContents) to control whether and how

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103 `Directory` listings should be loaded for use in expressions.

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104 * The position field of the [CommandLineBinding](#CommandLineBinding) can

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105 now be calculated from a CWL Expression.

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106 * The exit code of a CommandLineTool invocation is now

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107 available to expressions in `outputEval` as `runtime.exitCode`

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108 * [Better explain](#map) the `map<…>` notation that has existed since v1.0.

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109 * Fixed schema error where the `type` field inside the `inputs` and

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110 `outputs` field was incorrectly listed as optional.

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111 * For multi-Process CWL documents, if no particular process is named then

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112 the process with the `id` of `#main` is chosen.

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113

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114 See also the [CWL Workflow Description, v1.1.0-dev1 changelog](Workflow.html#Changelog).

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115

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116 ## Purpose

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117

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118 Standalone programs are a flexible and interoperable form of code reuse.

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119 Unlike monolithic applications, applications and analysis workflows which

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120 are composed of multiple separate programs can be written in multiple

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121 languages and execute concurrently on multiple hosts. However, POSIX

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122 does not dictate computer-readable grammar or semantics for program input

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123 and output, resulting in extremely heterogeneous command line grammar and

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124 input/output semantics among program. This is a particular problem in

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125 distributed computing (multi-node compute clusters) and virtualized

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126 environments (such as Docker containers) where it is often necessary to

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127 provision resources such as input files before executing the program.

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128

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129 Often this gap is filled by hard coding program invocation and

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130 implicitly assuming requirements will be met, or abstracting program

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131 invocation with wrapper scripts or descriptor documents. Unfortunately,

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132 where these approaches are application or platform specific it creates a

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133 significant barrier to reproducibility and portability, as methods

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134 developed for one platform must be manually ported to be used on new

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135 platforms. Similarly it creates redundant work, as wrappers for popular

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136 tools must be rewritten for each application or platform in use.

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137

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138 The Common Workflow Language Command Line Tool Description is designed to

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139 provide a common standard description of grammar and semantics for

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140 invoking programs used in data-intensive fields such as Bioinformatics,

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141 Chemistry, Physics, Astronomy, and Statistics. This specification

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142 attempts to define a precise data and execution model for Command Line Tools that

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143 can be implemented on a variety of computing platforms, ranging from a

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144 single workstation to cluster, grid, cloud, and high performance

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145 computing platforms. Details related to execution of these programs not

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146 laid out in this specification are open to interpretation by the computing

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147 platform implementing this specification.

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148

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149 - {$include: concepts.md}

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150 - {$include: invocation.md}

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151

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152

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153 - type: record

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154 name: EnvironmentDef

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155 doc: |

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156 Define an environment variable that will be set in the runtime environment

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157 by the workflow platform when executing the command line tool. May be the

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158 result of executing an expression, such as getting a parameter from input.

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159 fields:

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160 - name: envName

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161 type: string

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162 doc: The environment variable name

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163 - name: envValue

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164 type: [string, Expression]

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165 doc: The environment variable value

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166

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167 - type: record

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168 name: CommandLineBinding

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169 extends: InputBinding

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170 docParent: "#CommandInputParameter"

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171 doc: |

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172

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173 When listed under `inputBinding` in the input schema, the term

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174 "value" refers to the the corresponding value in the input object. For

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175 binding objects listed in `CommandLineTool.arguments`, the term "value"

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176 refers to the effective value after evaluating `valueFrom`.

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177

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178 The binding behavior when building the command line depends on the data

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179 type of the value. If there is a mismatch between the type described by

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180 the input schema and the effective value, such as resulting from an

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181 expression evaluation, an implementation must use the data type of the

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182 effective value.

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183

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184 - **string**: Add `prefix` and the string to the command line.

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185

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186 - **number**: Add `prefix` and decimal representation to command line.

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187

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188 - **boolean**: If true, add `prefix` to the command line. If false, add

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189 nothing.

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190

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191 - **File**: Add `prefix` and the value of

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192 [`File.path`](#File) to the command line.

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193

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194 - **Directory**: Add `prefix` and the value of

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195 [`Directory.path`](#Directory) to the command line.

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196

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197 - **array**: If `itemSeparator` is specified, add `prefix` and the join

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198 the array into a single string with `itemSeparator` separating the

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199 items. Otherwise first add `prefix`, then recursively process

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200 individual elements.

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201 If the array is empty, it does not add anything to command line.

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202

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203 - **object**: Add `prefix` only, and recursively add object fields for

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204 which `inputBinding` is specified.

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205

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206 - **null**: Add nothing.

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207

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208 fields:

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209 - name: position

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210 type: [ int, Expression, string, "null" ]

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211 doc: |

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212 The sorting key. Default position is 0. If the inputBinding is

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213 associated with an input parameter, then the value of `self` in the

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214 expression will be the value of the input parameter. Input parameter

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215 defaults (as specified by the `InputParameter.default` field) must be

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216 applied before evaluating the expression. Expressions must return a

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217 single value of type int or a null.

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218 - name: prefix

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219 type: string?

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220 doc: "Command line prefix to add before the value."

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221 - name: separate

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222 type: boolean?

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223 default: true

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224 doc: |

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225 If true (default), then the prefix and value must be added as separate

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226 command line arguments; if false, prefix and value must be concatenated

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227 into a single command line argument.

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228 - name: itemSeparator

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229 type: string?

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230 doc: |

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231 Join the array elements into a single string with the elements

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232 separated by by `itemSeparator`.

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233 - name: valueFrom

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234 type:

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235 - "null"

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236 - string

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237 - Expression

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238 jsonldPredicate: "cwl:valueFrom"

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239 doc: |

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240 If `valueFrom` is a constant string value, use this as the value and

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241 apply the binding rules above.

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242

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243 If `valueFrom` is an expression, evaluate the expression to yield the

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244 actual value to use to build the command line and apply the binding

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245 rules above. If the inputBinding is associated with an input

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246 parameter, the value of `self` in the expression will be the value of

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247 the input parameter. Input parameter defaults (as specified by the

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248 `InputParameter.default` field) must be applied before evaluating the

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249 expression.

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250

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251 If the value of the associated input parameter is `null`, `valueFrom` is

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252 not evaluated and nothing is added to the command line.

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253

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254 When a binding is part of the `CommandLineTool.arguments` field,

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255 the `valueFrom` field is required.

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256

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257 - name: shellQuote

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258 type: boolean?

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259 default: true

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260 doc: |

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261 If `ShellCommandRequirement` is in the requirements for the current command,

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262 this controls whether the value is quoted on the command line (default is true).

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263 Use `shellQuote: false` to inject metacharacters for operations such as pipes.

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264

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265 If `shellQuote` is true or not provided, the implementation must not

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266 permit interpretation of any shell metacharacters or directives.

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267

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268

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269 - type: record

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270 name: CommandOutputBinding

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271 extends: LoadContents

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272 doc: |

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273 Describes how to generate an output parameter based on the files produced

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274 by a CommandLineTool.

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275

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276 The output parameter value is generated by applying these operations in the

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277 following order:

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278

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279 - glob

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280 - loadContents

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281 - outputEval

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282 - secondaryFiles

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283 fields:

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284 - name: glob

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285 type:

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286 - "null"

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287 - string

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288 - Expression

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289 - type: array

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290 items: string

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291 doc: |

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292 Find files or directories relative to the output directory, using POSIX

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293 glob(3) pathname matching. If an array is provided, find files or

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294 directories that match any pattern in the array. If an expression is

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295 provided, the expression must return a string or an array of strings,

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296 which will then be evaluated as one or more glob patterns. Must only

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297 match and return files/directories which actually exist.

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298

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299 If the value of glob is a relative path pattern (does not

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300 begin with a slash '/') then it is resolved relative to the

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301 output directory. If the value of the glob is an absolute

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302 path pattern (it does begin with a slash '/') then it must

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303 refer to a path within the output directory. It is an error

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304 if any glob resolves to a path outside the output directory.

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305 Specifically this means globs with relative paths containing

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306 '..' or absolute paths that refer outside the output directory

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307 are illegal.

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308

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309 A glob may match a path within the output directory which is

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310 actually a symlink to another file. In this case, the

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311 expected behavior is for the resulting File/Directory object to take the

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312 `basename` (and corresponding `nameroot` and `nameext`) of the

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313 symlink. The `location` of the File/Directory is implementation

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314 dependent, but logically the File/Directory should have the same content

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315 as the symlink target. Platforms may stage output files/directories to

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316 cloud storage that lack the concept of a symlink. In

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317 this case file content and directories may be duplicated, or (to avoid

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318 duplication) the File/Directory `location` may refer to the symlink

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319 target.

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320

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321 It is an error if a symlink in the output directory (or any

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322 symlink in a chain of links) refers to any file or directory

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323 that is not under an input or output directory.

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324

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325 Implementations may shut down a container before globbing

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326 output, so globs and expressions must not assume access to the

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327 container filesystem except for declared input and output.

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328

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329 - name: outputEval

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330 type:

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331 - "null"

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332 - string

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333 - Expression

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334 doc: |

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335 Evaluate an expression to generate the output value. If

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336 `glob` was specified, the value of `self` must be an array

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337 containing file objects that were matched. If no files were

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338 matched, `self` must be a zero length array; if a single file

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339 was matched, the value of `self` is an array of a single

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340 element. Additionally, if `loadContents` is `true`, the File

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341 objects must include up to the first 64 KiB of file contents

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342 in the `contents` field. The exit code of the process is

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343 available in the expression as `runtime.exitCode`.

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344

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345 - name: CommandLineBindable

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346 type: record

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347 fields:

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348 inputBinding:

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349 type: CommandLineBinding?

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350 jsonldPredicate: "cwl:inputBinding"

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351 doc: Describes how to turn this object into command line arguments.

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352

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353 - name: CommandInputRecordField

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354 type: record

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355 extends: [InputRecordField, CommandLineBindable]

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356 specialize:

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357 - specializeFrom: InputRecordSchema

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358 specializeTo: CommandInputRecordSchema

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359 - specializeFrom: InputEnumSchema

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360 specializeTo: CommandInputEnumSchema

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361 - specializeFrom: InputArraySchema

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362 specializeTo: CommandInputArraySchema

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363 - specializeFrom: InputBinding

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364 specializeTo: CommandLineBinding

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365

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366

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367 - name: CommandInputRecordSchema

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368 type: record

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369 extends: [InputRecordSchema, CommandInputSchema, CommandLineBindable]

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370 specialize:

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371 - specializeFrom: InputRecordField

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372 specializeTo: CommandInputRecordField

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373 - specializeFrom: InputBinding

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374 specializeTo: CommandLineBinding

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375

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376

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377 - name: CommandInputEnumSchema

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378 type: record

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379 extends: [InputEnumSchema, CommandInputSchema, CommandLineBindable]

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380 specialize:

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381 - specializeFrom: InputBinding

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382 specializeTo: CommandLineBinding

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383

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384

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385 - name: CommandInputArraySchema

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386 type: record

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387 extends: [InputArraySchema, CommandInputSchema, CommandLineBindable]

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388 specialize:

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389 - specializeFrom: InputRecordSchema

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390 specializeTo: CommandInputRecordSchema

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391 - specializeFrom: InputEnumSchema

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392 specializeTo: CommandInputEnumSchema

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393 - specializeFrom: InputArraySchema

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394 specializeTo: CommandInputArraySchema

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395 - specializeFrom: InputBinding

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396 specializeTo: CommandLineBinding

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397

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398

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399 - name: CommandOutputRecordField

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400 type: record

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401 extends: OutputRecordField

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402 specialize:

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403 - specializeFrom: OutputRecordSchema

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404 specializeTo: CommandOutputRecordSchema

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405 - specializeFrom: OutputEnumSchema

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406 specializeTo: CommandOutputEnumSchema

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407 - specializeFrom: OutputArraySchema

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408 specializeTo: CommandOutputArraySchema

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409 fields:

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410 - name: outputBinding

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411 type: CommandOutputBinding?

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412 jsonldPredicate: "cwl:outputBinding"

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413 doc: |

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414 Describes how to generate this output object based on the files

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415 produced by a CommandLineTool

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416

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417

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418 - name: CommandOutputRecordSchema

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419 type: record

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420 extends: OutputRecordSchema

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421 specialize:

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422 - specializeFrom: OutputRecordField

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423 specializeTo: CommandOutputRecordField

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424

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425

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426 - name: CommandOutputEnumSchema

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427 type: record

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428 extends: OutputEnumSchema

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429 specialize:

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430 - specializeFrom: OutputRecordSchema

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431 specializeTo: CommandOutputRecordSchema

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432 - specializeFrom: OutputEnumSchema

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433 specializeTo: CommandOutputEnumSchema

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434 - specializeFrom: OutputArraySchema

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435 specializeTo: CommandOutputArraySchema

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436

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437

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438 - name: CommandOutputArraySchema

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439 type: record

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440 extends: OutputArraySchema

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441 specialize:

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442 - specializeFrom: OutputRecordSchema

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443 specializeTo: CommandOutputRecordSchema

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444 - specializeFrom: OutputEnumSchema

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445 specializeTo: CommandOutputEnumSchema

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446 - specializeFrom: OutputArraySchema

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447 specializeTo: CommandOutputArraySchema

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448

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449

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450 - type: record

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451 name: CommandInputParameter

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452 extends: InputParameter

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453 doc: An input parameter for a CommandLineTool.

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454 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

455 - name: type

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

456 type:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

457 - CWLType

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

458 - stdin

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

459 - CommandInputRecordSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

460 - CommandInputEnumSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

461 - CommandInputArraySchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

462 - string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

463 - type: array

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

464 items:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

465 - CWLType

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

466 - CommandInputRecordSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

467 - CommandInputEnumSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

468 - CommandInputArraySchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

469 - string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

470 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

471 "_id": "sld:type"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

472 "_type": "@vocab"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

473 refScope: 2

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

474 typeDSL: True

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

475 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

476 Specify valid types of data that may be assigned to this parameter.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

477 - name: inputBinding

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

478 type: CommandLineBinding?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

479 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

480 Describes how to turns the input parameters of a process into

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

481 command line arguments.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

482 jsonldPredicate: "cwl:inputBinding"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

483

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

484 - type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

485 name: CommandOutputParameter

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

486 extends: OutputParameter

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

487 doc: An output parameter for a CommandLineTool.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

488 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

489 - name: type

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

490 type:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

491 - CWLType

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

492 - stdout

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

493 - stderr

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

494 - CommandOutputRecordSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

495 - CommandOutputEnumSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

496 - CommandOutputArraySchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

497 - string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

498 - type: array

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

499 items:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

500 - CWLType

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

501 - CommandOutputRecordSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

502 - CommandOutputEnumSchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

503 - CommandOutputArraySchema

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

504 - string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

505 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

506 "_id": "sld:type"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

507 "_type": "@vocab"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

508 refScope: 2

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

509 typeDSL: True

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

510 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

511 Specify valid types of data that may be assigned to this parameter.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

512 - name: outputBinding

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

513 type: CommandOutputBinding?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

514 jsonldPredicate: "cwl:outputBinding"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

515 doc: Describes how to generate this output object based on the files

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

516 produced by a CommandLineTool

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

517

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

518 - name: stdin

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

519 type: enum

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

520 symbols: [ "cwl:stdin" ]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

521 docParent: "#CommandOutputParameter"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

522 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

523 Only valid as a `type` for a `CommandLineTool` input with no

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

524 `inputBinding` set. `stdin` must not be specified at the `CommandLineTool`

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

525 level.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

526

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

527 The following

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

528 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

529 inputs:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

530 an_input_name:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

531 type: stdin

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

532 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

533 is equivalent to

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

534 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

535 inputs:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

536 an_input_name:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

537 type: File

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

538 streamable: true

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

539

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

540 stdin: ${inputs.an_input_name.path}

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

541 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

542

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

543 - name: stdout

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

544 type: enum

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

545 symbols: [ "cwl:stdout" ]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

546 docParent: "#CommandOutputParameter"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

547 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

548 Only valid as a `type` for a `CommandLineTool` output with no

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

549 `outputBinding` set.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

550

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

551 The following

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

552 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

553 outputs:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

554 an_output_name:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

555 type: stdout

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

556

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

557 stdout: a_stdout_file

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

558 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

559 is equivalent to

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

560 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

561 outputs:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

562 an_output_name:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

563 type: File

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

564 streamable: true

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

565 outputBinding:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

566 glob: a_stdout_file

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

567

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

568 stdout: a_stdout_file

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

569 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

570

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

571 If there is no `stdout` name provided, a random filename will be created.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

572 For example, the following

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

573 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

574 outputs:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

575 an_output_name:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

576 type: stdout

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

577 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

578 is equivalent to

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

579 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

580 outputs:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

581 an_output_name:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

582 type: File

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

583 streamable: true

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

584 outputBinding:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

585 glob: random_stdout_filenameABCDEFG

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

586

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

587 stdout: random_stdout_filenameABCDEFG

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

588 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

589

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

590

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

591 - name: stderr

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diff changeset

592 type: enum

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diff changeset

593 symbols: [ "cwl:stderr" ]

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diff changeset

594 docParent: "#CommandOutputParameter"

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595 doc: |

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596 Only valid as a `type` for a `CommandLineTool` output with no

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597 `outputBinding` set.

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598

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599 The following

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600 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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601 outputs:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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602 an_output_name:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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603 type: stderr

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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diff changeset

604

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

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diff changeset

605 stderr: a_stderr_file

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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diff changeset

606 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

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diff changeset

607 is equivalent to

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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diff changeset

608 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

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diff changeset

609 outputs:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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diff changeset

610 an_output_name:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

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diff changeset

611 type: File

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

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diff changeset

612 streamable: true

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

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diff changeset

613 outputBinding:

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shellac

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diff changeset

614 glob: a_stderr_file

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diff changeset

615

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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diff changeset

616 stderr: a_stderr_file

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

617 ```

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shellac

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diff changeset

618

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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diff changeset

619 If there is no `stderr` name provided, a random filename will be created.

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620 For example, the following

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621 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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diff changeset

622 outputs:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

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diff changeset

623 an_output_name:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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diff changeset

624 type: stderr

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

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diff changeset

625 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

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diff changeset

626 is equivalent to

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

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diff changeset

627 ```

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

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diff changeset

628 outputs:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

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diff changeset

629 an_output_name:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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diff changeset

630 type: File

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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diff changeset

631 streamable: true

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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632 outputBinding:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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633 glob: random_stderr_filenameABCDEFG

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diff changeset

634

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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635 stderr: random_stderr_filenameABCDEFG

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diff changeset

636 ```

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diff changeset

637

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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diff changeset

638

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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diff changeset

639 - type: record

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diff changeset

640 name: CommandLineTool

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

641 extends: Process

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

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diff changeset

642 documentRoot: true

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

643 specialize:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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diff changeset

644 - specializeFrom: InputParameter

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diff changeset

645 specializeTo: CommandInputParameter

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parents:

diff changeset

646 - specializeFrom: OutputParameter

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diff changeset

647 specializeTo: CommandOutputParameter

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648 doc: |

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diff changeset

649 This defines the schema of the CWL Command Line Tool Description document.

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parents:

diff changeset

650

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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651 fields:

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diff changeset

652 - name: class

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653 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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diff changeset

654 "_id": "@type"

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diff changeset

655 "_type": "@vocab"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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diff changeset

656 type: string

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parents:

diff changeset

657 - name: baseCommand

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658 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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diff changeset

659 Specifies the program to execute. If an array, the first element of

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

660 the array is the command to execute, and subsequent elements are

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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diff changeset

661 mandatory command line arguments. The elements in `baseCommand` must

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shellac

parents:

diff changeset

662 appear before any command line bindings from `inputBinding` or

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shellac

parents:

diff changeset

663 `arguments`.

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shellac

parents:

diff changeset

664

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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diff changeset

665 If `baseCommand` is not provided or is an empty array, the first

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

666 element of the command line produced after processing `inputBinding` or

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shellac

parents:

diff changeset

667 `arguments` must be used as the program to execute.

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shellac

parents:

diff changeset

668

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

669 If the program includes a path separator character it must

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

670 be an absolute path, otherwise it is an error. If the program does not

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

671 include a path separator, search the `$PATH` variable in the runtime

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

672 environment of the workflow runner find the absolute path of the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

673 executable.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

674 type:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

675 - string?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

676 - string[]?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

677 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

678 "_id": "cwl:baseCommand"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

679 "_container": "@list"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

680 - name: arguments

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parents:

diff changeset

681 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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diff changeset

682 Command line bindings which are not directly associated with input

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

683 parameters. If the value is a string, it is used as a string literal

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parents:

diff changeset

684 argument. If it is an Expression, the result of the evaluation is used

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parents:

diff changeset

685 as an argument.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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diff changeset

686 type:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

687 - "null"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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diff changeset

688 - type: array

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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diff changeset

689 items: [string, Expression, CommandLineBinding]

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diff changeset

690 jsonldPredicate:

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parents:

diff changeset

691 "_id": "cwl:arguments"

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parents:

diff changeset

692 "_container": "@list"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

693 - name: stdin

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

694 type: ["null", string, Expression]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

695 jsonldPredicate: "https://w3id.org/cwl/cwl#stdin"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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diff changeset

696 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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diff changeset

697 A path to a file whose contents must be piped into the command's

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parents:

diff changeset

698 standard input stream.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

699 - name: stderr

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

700 type: ["null", string, Expression]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

701 jsonldPredicate: "https://w3id.org/cwl/cwl#stderr"

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702 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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diff changeset

703 Capture the command's standard error stream to a file written to

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shellac

parents:

diff changeset

704 the designated output directory.

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parents:

diff changeset

705

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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diff changeset

706 If `stderr` is a string, it specifies the file name to use.

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diff changeset

707

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diff changeset

708 If `stderr` is an expression, the expression is evaluated and must

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

709 return a string with the file name to use to capture stderr. If the

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parents:

diff changeset

710 return value is not a string, or the resulting path contains illegal

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diff changeset

711 characters (such as the path separator `/`) it is an error.

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parents:

diff changeset

712 - name: stdout

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713 type: ["null", string, Expression]

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diff changeset

714 jsonldPredicate: "https://w3id.org/cwl/cwl#stdout"

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715 doc: |

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diff changeset

716 Capture the command's standard output stream to a file written to

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parents:

diff changeset

717 the designated output directory.

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parents:

diff changeset

718

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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diff changeset

719 If `stdout` is a string, it specifies the file name to use.

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diff changeset

720

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diff changeset

721 If `stdout` is an expression, the expression is evaluated and must

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

722 return a string with the file name to use to capture stdout. If the

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shellac

parents:

diff changeset

723 return value is not a string, or the resulting path contains illegal

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

724 characters (such as the path separator `/`) it is an error.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

725 - name: successCodes

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

726 type: int[]?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

727 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

728 Exit codes that indicate the process completed successfully.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

729

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

730 - name: temporaryFailCodes

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

731 type: int[]?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

732 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

733 Exit codes that indicate the process failed due to a possibly

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

734 temporary condition, where executing the process with the same

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

735 runtime environment and inputs may produce different results.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

736

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

737 - name: permanentFailCodes

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

738 type: int[]?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

739 doc:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

740 Exit codes that indicate the process failed due to a permanent logic

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

741 error, where executing the process with the same runtime environment and

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

742 same inputs is expected to always fail.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

743

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

744

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

745 - type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

746 name: DockerRequirement

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

747 extends: ProcessRequirement

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

748 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

749 Indicates that a workflow component should be run in a

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

750 [Docker](http://docker.com) or Docker-compatible (such as

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

751 [Singularity](https://www.sylabs.io/) and [udocker](https://github.com/indigo-dc/udocker)) container environment and

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

752 specifies how to fetch or build the image.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

753

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

754 If a CommandLineTool lists `DockerRequirement` under

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

755 `hints` (or `requirements`), it may (or must) be run in the specified Docker

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

756 container.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

757

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

758 The platform must first acquire or install the correct Docker image as

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

759 specified by `dockerPull`, `dockerImport`, `dockerLoad` or `dockerFile`.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

760

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

761 The platform must execute the tool in the container using `docker run` with

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

762 the appropriate Docker image and tool command line.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

763

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

764 The workflow platform may provide input files and the designated output

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

765 directory through the use of volume bind mounts. The platform should rewrite

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

766 file paths in the input object to correspond to the Docker bind mounted

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

767 locations. That is, the platform should rewrite values in the parameter context

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

768 such as `runtime.outdir`, `runtime.tmpdir` and others to be valid paths

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

769 within the container. The platform must ensure that `runtime.outdir` and

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

770 `runtime.tmpdir` are distinct directories.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

771

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

772 When running a tool contained in Docker, the workflow platform must not

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

773 assume anything about the contents of the Docker container, such as the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

774 presence or absence of specific software, except to assume that the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

775 generated command line represents a valid command within the runtime

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

776 environment of the container.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

777

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

778 A container image may specify an

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

779 [ENTRYPOINT](https://docs.docker.com/engine/reference/builder/#entrypoint)

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

780 and/or

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

781 [CMD](https://docs.docker.com/engine/reference/builder/#cmd).

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

782 Command line arguments will be appended after all elements of

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

783 ENTRYPOINT, and will override all elements specified using CMD (in

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

784 other words, CMD is only used when the CommandLineTool definition

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

785 produces an empty command line).

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

786

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

787 Use of implicit ENTRYPOINT or CMD are discouraged due to reproducibility

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

788 concerns of the implicit hidden execution point (For further discussion, see

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

789 [https://doi.org/10.12688/f1000research.15140.1](https://doi.org/10.12688/f1000research.15140.1)). Portable

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

790 CommandLineTool wrappers in which use of a container is optional must not rely on ENTRYPOINT or CMD.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

791 CommandLineTools which do rely on ENTRYPOINT or CMD must list `DockerRequirement` in the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

792 `requirements` section.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

793

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

794 ## Interaction with other requirements

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shellac

parents:

diff changeset

795

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

796 If [EnvVarRequirement](#EnvVarRequirement) is specified alongside a

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

797 DockerRequirement, the environment variables must be provided to Docker

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

798 using `--env` or `--env-file` and interact with the container's preexisting

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shellac

parents:

diff changeset

799 environment as defined by Docker.

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shellac

parents:

diff changeset

800

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

801 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

802 - name: class

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

803 type: string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

804 doc: "Always 'DockerRequirement'"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

805 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

806 "_id": "@type"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

807 "_type": "@vocab"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

808 - name: dockerPull

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

809 type: string?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

810 doc: "Specify a Docker image to retrieve using `docker pull`."

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

811 - name: dockerLoad

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

812 type: string?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

813 doc: "Specify a HTTP URL from which to download a Docker image using `docker load`."

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

814 - name: dockerFile

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

815 type: string?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

816 doc: "Supply the contents of a Dockerfile which will be built using `docker build`."

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shellac

parents:

diff changeset

817 - name: dockerImport

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shellac

parents:

diff changeset

818 type: string?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

819 doc: "Provide HTTP URL to download and gunzip a Docker images using `docker import."

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shellac

parents:

diff changeset

820 - name: dockerImageId

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

821 type: string?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

822 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

823 The image id that will be used for `docker run`. May be a

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

824 human-readable image name or the image identifier hash. May be skipped

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

825 if `dockerPull` is specified, in which case the `dockerPull` image id

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

826 must be used.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

827 - name: dockerOutputDirectory

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

828 type: string?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

829 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

830 Set the designated output directory to a specific location inside the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

831 Docker container.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

832

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

833

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

834 - type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

835 name: SoftwareRequirement

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

836 extends: ProcessRequirement

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

837 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

838 A list of software packages that should be configured in the environment of

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

839 the defined process.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

840 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

841 - name: class

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

842 type: string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

843 doc: "Always 'SoftwareRequirement'"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

844 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

845 "_id": "@type"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

846 "_type": "@vocab"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

847 - name: packages

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

848 type: SoftwarePackage[]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

849 doc: "The list of software to be configured."

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

850 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

851 mapSubject: package

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

852 mapPredicate: specs

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

853

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

854 - name: SoftwarePackage

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

855 type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

856 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

857 - name: package

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

858 type: string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

859 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

860 The name of the software to be made available. If the name is

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

861 common, inconsistent, or otherwise ambiguous it should be combined with

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

862 one or more identifiers in the `specs` field.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

863 - name: version

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

864 type: string[]?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

865 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

866 The (optional) versions of the software that are known to be

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

867 compatible.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

868 - name: specs

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

869 type: string[]?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

870 jsonldPredicate: {_type: "@id", noLinkCheck: true}

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

871 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

872 One or more [IRI](https://en.wikipedia.org/wiki/Internationalized_Resource_Identifier)s

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

873 identifying resources for installing or enabling the software named in

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shellac

parents:

diff changeset

874 the `package` field. Implementations may provide resolvers which map

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

875 these software identifer IRIs to some configuration action; or they can

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

876 use only the name from the `package` field on a best effort basis.

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shellac

parents:

diff changeset

877

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shellac

parents:

diff changeset

878 For example, the IRI https://packages.debian.org/bowtie could

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parents:

diff changeset

879 be resolved with `apt-get install bowtie`. The IRI

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

880 https://anaconda.org/bioconda/bowtie could be resolved with `conda

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

881 install -c bioconda bowtie`.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

882

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

883 IRIs can also be system independent and used to map to a specific

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

884 software installation or selection mechanism.

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parents:

diff changeset

885 Using [RRID](https://www.identifiers.org/rrid/) as an example:

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shellac

parents:

diff changeset

886 https://identifiers.org/rrid/RRID:SCR_005476

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shellac

parents:

diff changeset

887 could be fulfilled using the above mentioned Debian or bioconda

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

888 package, a local installation managed by [Environement Modules](http://modules.sourceforge.net/),

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

889 or any other mechanism the platform chooses. IRIs can also be from

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

890 identifer sources that are discipline specific yet still system

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

891 independent. As an example, the equivalent [ELIXIR Tools and Data

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

892 Service Registry](https://bio.tools) IRI to the previous RRID example is

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

893 https://bio.tools/tool/bowtie2/version/2.2.8.

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shellac

parents:

diff changeset

894 If supported by a given registry, implementations are encouraged to

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

895 query these system independent sofware identifier IRIs directly for

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

896 links to packaging systems.

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parents:

diff changeset

897

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

898 A site specific IRI can be listed as well. For example, an academic

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

899 computing cluster using Environement Modules could list the IRI

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

900 `https://hpc.example.edu/modules/bowtie-tbb/1.22` to indicate that

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

901 `module load bowtie-tbb/1.1.2` should be executed to make available

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shellac

parents:

diff changeset

902 `bowtie` version 1.1.2 compiled with the TBB library prior to running

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

903 the accompanying Workflow or CommandLineTool. Note that the example IRI

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

904 is specific to a particular institution and computing environment as

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

905 the Environment Modules system does not have a common namespace or

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

906 standardized naming convention.

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shellac

parents:

diff changeset

907

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

908 This last example is the least portable and should only be used if

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

909 mechanisms based off of the `package` field or more generic IRIs are

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

910 unavailable or unsuitable. While harmless to other sites, site specific

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

911 software IRIs should be left out of shared CWL descriptions to avoid

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

912 clutter.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

913

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

914 - name: Dirent

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

915 type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

916 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

917 Define a file or subdirectory that must be placed in the designated output

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

918 directory prior to executing the command line tool. May be the result of

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

919 executing an expression, such as building a configuration file from a

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

920 template.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

921 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

922 - name: entryname

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

923 type: ["null", string, Expression]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

924 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

925 _id: cwl:entryname

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

926 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

927 The name of the file or subdirectory to create in the output directory.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

928 If `entry` is a File or Directory, the `entryname` field overrides the value

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

929 of `basename` of the File or Directory object. Optional.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

930 - name: entry

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

931 type: [string, Expression]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

932 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

933 _id: cwl:entry

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

934 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

935 If the value is a string literal or an expression which evaluates to a

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

936 string, a new file must be created with the string as the file contents.

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shellac

parents:

diff changeset

937

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

938 If the value is an expression that evaluates to a `File` object, this

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

939 indicates the referenced file should be added to the designated output

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

940 directory prior to executing the tool.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

941

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

942 If the value is an expression that evaluates to a `Dirent` object, this

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

943 indicates that the File or Directory in `entry` should be added to the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

944 designated output directory with the name in `entryname`.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

945

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parents:

diff changeset

946 If `writable` is false, the file may be made available using a bind

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

947 mount or file system link to avoid unnecessary copying of the input

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

948 file.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

949 - name: writable

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

950 type: boolean?

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

951 default: false

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

952 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

953 If true, the file or directory must be writable by the tool. Changes

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

954 to the file or directory must be isolated and not visible by any other

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

955 CommandLineTool process. This may be implemented by making a copy of

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

956 the original file or directory. Default false (files and directories

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

957 read-only by default).

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

958

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

959 A directory marked as `writable: true` implies that all files and

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

960 subdirectories are recursively writable as well.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

961

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

962

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

963 - name: InitialWorkDirRequirement

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

964 type: record

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

965 extends: ProcessRequirement

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

966 doc:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

967 Define a list of files and subdirectories that must be created by the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

968 workflow platform in the designated output directory prior to executing the

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

969 command line tool.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

970 fields:

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shellac

parents:

diff changeset

971 - name: class

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

972 type: string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

973 doc: InitialWorkDirRequirement

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

974 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

975 "_id": "@type"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

976 "_type": "@vocab"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

977 - name: listing

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shellac

parents:

diff changeset

978 type:

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shellac

parents:

diff changeset

979 - type: array

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shellac

parents:

diff changeset

980 items:

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shellac

parents:

diff changeset

981 - "null"

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shellac

parents:

diff changeset

982 - File

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shellac

parents:

diff changeset

983 - type: array

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shellac

parents:

diff changeset

984 items:

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shellac

parents:

diff changeset

985 - File

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shellac

parents:

diff changeset

986 - Directory

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shellac

parents:

diff changeset

987 - Directory

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shellac

parents:

diff changeset

988 - Dirent

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shellac

parents:

diff changeset

989 - string

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parents:

diff changeset

990 - Expression

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parents:

diff changeset

991 - string

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parents:

diff changeset

992 - Expression

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

993 jsonldPredicate:

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parents:

diff changeset

994 _id: "cwl:listing"

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parents:

diff changeset

995 doc: |

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parents:

diff changeset

996 The list of files or subdirectories that must be placed in the

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shellac

parents:

diff changeset

997 designated output directory prior to executing the command line tool.

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shellac

parents:

diff changeset

998

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parents:

diff changeset

999 May be an expression. If so, the expression return value must validate as

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parents:

diff changeset

1000 `{type: array, items: ["null", File, File[], Directory, Directory[], Dirent]}`.

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parents:

diff changeset

1001

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parents:

diff changeset

1002 Files or Directories which are listed in the input parameters and

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parents:

diff changeset

1003 appear in the `InitialWorkDirRequirement` listing must have their

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parents:

diff changeset

1004 `path` set to their staged location in the designated output directory.

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shellac

parents:

diff changeset

1005 If the same File or Directory appears more than once in the

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parents:

diff changeset

1006 `InitialWorkDirRequirement` listing, the implementation must choose

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shellac

parents:

diff changeset

1007 exactly one value for `path`; how this value is chosen is undefined.

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parents:

diff changeset

1008

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parents:

diff changeset

1009

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parents:

diff changeset

1010 - name: EnvVarRequirement

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shellac

parents:

diff changeset

1011 type: record

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parents:

diff changeset

1012 extends: ProcessRequirement

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parents:

diff changeset

1013 doc: |

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parents:

diff changeset

1014 Define a list of environment variables which will be set in the

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shellac

parents:

diff changeset

1015 execution environment of the tool. See `EnvironmentDef` for details.

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parents:

diff changeset

1016 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1017 - name: class

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1018 type: string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

1019 doc: "Always 'EnvVarRequirement'"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

1020 jsonldPredicate:

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parents:

diff changeset

1021 "_id": "@type"

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parents:

diff changeset

1022 "_type": "@vocab"

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parents:

diff changeset

1023 - name: envDef

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parents:

diff changeset

1024 type: EnvironmentDef[]

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parents:

diff changeset

1025 doc: The list of environment variables.

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parents:

diff changeset

1026 jsonldPredicate:

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parents:

diff changeset

1027 mapSubject: envName

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parents:

diff changeset

1028 mapPredicate: envValue

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parents:

diff changeset

1029

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parents:

diff changeset

1030

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parents:

diff changeset

1031 - type: record

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parents:

diff changeset

1032 name: ShellCommandRequirement

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parents:

diff changeset

1033 extends: ProcessRequirement

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parents:

diff changeset

1034 doc: |

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parents:

diff changeset

1035 Modify the behavior of CommandLineTool to generate a single string

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parents:

diff changeset

1036 containing a shell command line. Each item in the argument list must be

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shellac

parents:

diff changeset

1037 joined into a string separated by single spaces and quoted to prevent

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shellac

parents:

diff changeset

1038 intepretation by the shell, unless `CommandLineBinding` for that argument

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shellac

parents:

diff changeset

1039 contains `shellQuote: false`. If `shellQuote: false` is specified, the

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shellac

parents:

diff changeset

1040 argument is joined into the command string without quoting, which allows

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1041 the use of shell metacharacters such as `|` for pipes.

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shellac

parents:

diff changeset

1042 fields:

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shellac

parents:

diff changeset

1043 - name: class

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1044 type: string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1045 doc: "Always 'ShellCommandRequirement'"

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shellac

parents:

diff changeset

1046 jsonldPredicate:

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shellac

parents:

diff changeset

1047 "_id": "@type"

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shellac

parents:

diff changeset

1048 "_type": "@vocab"

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parents:

diff changeset

1049

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parents:

diff changeset

1050

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parents:

diff changeset

1051 - type: record

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shellac

parents:

diff changeset

1052 name: ResourceRequirement

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shellac

parents:

diff changeset

1053 extends: ProcessRequirement

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shellac

parents:

diff changeset

1054 doc: |

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shellac

parents:

diff changeset

1055 Specify basic hardware resource requirements.

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shellac

parents:

diff changeset

1056

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parents:

diff changeset

1057 "min" is the minimum amount of a resource that must be reserved to schedule

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shellac

parents:

diff changeset

1058 a job. If "min" cannot be satisfied, the job should not be run.

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shellac

parents:

diff changeset

1059

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parents:

diff changeset

1060 "max" is the maximum amount of a resource that the job shall be permitted

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shellac

parents:

diff changeset

1061 to use. If a node has sufficient resources, multiple jobs may be scheduled

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shellac

parents:

diff changeset

1062 on a single node provided each job's "max" resource requirements are

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1063 met. If a job attempts to exceed its "max" resource allocation, an

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shellac

parents:

diff changeset

1064 implementation may deny additional resources, which may result in job

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parents:

diff changeset

1065 failure.

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parents:

diff changeset

1066

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parents:

diff changeset

1067 If "min" is specified but "max" is not, then "max" == "min"

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shellac

parents:

diff changeset

1068 If "max" is specified by "min" is not, then "min" == "max".

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parents:

diff changeset

1069

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parents:

diff changeset

1070 It is an error if max < min.

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parents:

diff changeset

1071

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parents:

diff changeset

1072 It is an error if the value of any of these fields is negative.

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parents:

diff changeset

1073

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parents:

diff changeset

1074 If neither "min" nor "max" is specified for a resource, an implementation may provide a default.

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parents:

diff changeset

1075

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parents:

diff changeset

1076 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1077 - name: class

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1078 type: string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1079 doc: "Always 'ResourceRequirement'"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1080 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1081 "_id": "@type"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1082 "_type": "@vocab"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

1083 - name: coresMin

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parents:

diff changeset

1084 type: ["null", long, string, Expression]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1085 doc: Minimum reserved number of CPU cores

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parents:

diff changeset

1086

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parents:

diff changeset

1087 - name: coresMax

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parents:

diff changeset

1088 type: ["null", int, string, Expression]

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shellac

parents:

diff changeset

1089 doc: Maximum reserved number of CPU cores

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shellac

parents:

diff changeset

1090

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parents:

diff changeset

1091 - name: ramMin

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parents:

diff changeset

1092 type: ["null", long, string, Expression]

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parents:

diff changeset

1093 doc: Minimum reserved RAM in mebibytes (2**20)

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parents:

diff changeset

1094

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parents:

diff changeset

1095 - name: ramMax

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parents:

diff changeset

1096 type: ["null", long, string, Expression]

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parents:

diff changeset

1097 doc: Maximum reserved RAM in mebibytes (2**20)

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parents:

diff changeset

1098

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parents:

diff changeset

1099 - name: tmpdirMin

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parents:

diff changeset

1100 type: ["null", long, string, Expression]

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shellac

parents:

diff changeset

1101 doc: Minimum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)

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parents:

diff changeset

1102

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parents:

diff changeset

1103 - name: tmpdirMax

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parents:

diff changeset

1104 type: ["null", long, string, Expression]

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shellac

parents:

diff changeset

1105 doc: Maximum reserved filesystem based storage for the designated temporary directory, in mebibytes (2**20)

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shellac

parents:

diff changeset

1106

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shellac

parents:

diff changeset

1107 - name: outdirMin

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shellac

parents:

diff changeset

1108 type: ["null", long, string, Expression]

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parents:

diff changeset

1109 doc: Minimum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)

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parents:

diff changeset

1110

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diff changeset

1111 - name: outdirMax

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parents:

diff changeset

1112 type: ["null", long, string, Expression]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1113 doc: Maximum reserved filesystem based storage for the designated output directory, in mebibytes (2**20)

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parents:

diff changeset

1114

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parents:

diff changeset

1115

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parents:

diff changeset

1116 - type: record

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parents:

diff changeset

1117 name: WorkReuse

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parents:

diff changeset

1118 extends: ProcessRequirement

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parents:

diff changeset

1119 doc: |

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parents:

diff changeset

1120 For implementations that support reusing output from past work (on

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shellac

parents:

diff changeset

1121 the assumption that same code and same input produce same

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1122 results), control whether to enable or disable the reuse behavior

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shellac

parents:

diff changeset

1123 for a particular tool or step (to accomodate situations where that

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shellac

parents:

diff changeset

1124 assumption is incorrect). A reused step is not executed but

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shellac

parents:

diff changeset

1125 instead returns the same output as the original execution.

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parents:

diff changeset

1126

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parents:

diff changeset

1127 If `enableReuse` is not specified, correct tools should assume it

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parents:

diff changeset

1128 is enabled by default.

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parents:

diff changeset

1129 fields:

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parents:

diff changeset

1130 - name: class

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parents:

diff changeset

1131 type: string

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parents:

diff changeset

1132 doc: "Always 'WorkReuse'"

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parents:

diff changeset

1133 jsonldPredicate:

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parents:

diff changeset

1134 "_id": "@type"

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parents:

diff changeset

1135 "_type": "@vocab"

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parents:

diff changeset

1136 - name: enableReuse

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parents:

diff changeset

1137 type: [boolean, string, Expression]

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parents:

diff changeset

1138 default: true

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diff changeset

1139

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parents:

diff changeset

1140

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parents:

diff changeset

1141 - type: record

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parents:

diff changeset

1142 name: NetworkAccess

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parents:

diff changeset

1143 extends: ProcessRequirement

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parents:

diff changeset

1144 doc: |

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parents:

diff changeset

1145 Indicate whether a process requires outgoing IPv4/IPv6 network

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shellac

parents:

diff changeset

1146 access. Choice of IPv4 or IPv6 is implementation and site

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parents:

diff changeset

1147 specific, correct tools must support both.

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parents:

diff changeset

1148

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parents:

diff changeset

1149 If `networkAccess` is false or not specified, tools must not

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shellac

parents:

diff changeset

1150 assume network access, except for localhost (the loopback device).

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parents:

diff changeset

1151

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parents:

diff changeset

1152 If `networkAccess` is true, the tool must be able to make outgoing

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shellac

parents:

diff changeset

1153 connections to network resources. Resources may be on a private

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shellac

parents:

diff changeset

1154 subnet or the public Internet. However, implementations and sites

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1155 may apply their own security policies to restrict what is

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parents:

diff changeset

1156 accessible by the tool.

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parents:

diff changeset

1157

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parents:

diff changeset

1158 Enabling network access does not imply a publically routable IP

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shellac

parents:

diff changeset

1159 address or the ability to accept inbound connections.

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shellac

parents:

diff changeset

1160

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parents:

diff changeset

1161 fields:

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parents:

diff changeset

1162 - name: class

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parents:

diff changeset

1163 type: string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1164 doc: "Always 'NetworkAccess'"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1165 jsonldPredicate:

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parents:

diff changeset

1166 "_id": "@type"

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parents:

diff changeset

1167 "_type": "@vocab"

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parents:

diff changeset

1168 - name: networkAccess

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parents:

diff changeset

1169 type: [boolean, string, Expression]

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parents:

diff changeset

1170

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parents:

diff changeset

1171 - name: InplaceUpdateRequirement

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parents:

diff changeset

1172 type: record

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shellac

parents:

diff changeset

1173 extends: cwl:ProcessRequirement

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parents:

diff changeset

1174 doc: |

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shellac

parents:

diff changeset

1175

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shellac

parents:

diff changeset

1176 If `inplaceUpdate` is true, then an implementation supporting this

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shellac

parents:

diff changeset

1177 feature may permit tools to directly update files with `writable:

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shellac

parents:

diff changeset

1178 true` in InitialWorkDirRequirement. That is, as an optimization,

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shellac

parents:

diff changeset

1179 files may be destructively modified in place as opposed to copied

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shellac

parents:

diff changeset

1180 and updated.

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shellac

parents:

diff changeset

1181

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shellac

parents:

diff changeset

1182 An implementation must ensure that only one workflow step may

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shellac

parents:

diff changeset

1183 access a writable file at a time. It is an error if a file which

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shellac

parents:

diff changeset

1184 is writable by one workflow step file is accessed (for reading or

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shellac

parents:

diff changeset

1185 writing) by any other workflow step running independently.

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shellac

parents:

diff changeset

1186 However, a file which has been updated in a previous completed

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shellac

parents:

diff changeset

1187 step may be used as input to multiple steps, provided it is

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shellac

parents:

diff changeset

1188 read-only in every step.

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shellac

parents:

diff changeset

1189

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shellac

parents:

diff changeset

1190 Workflow steps which modify a file must produce the modified file

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shellac

parents:

diff changeset

1191 as output. Downstream steps which futher process the file must

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shellac

parents:

diff changeset

1192 use the output of previous steps, and not refer to a common input

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1193 (this is necessary for both ordering and correctness).

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shellac

parents:

diff changeset

1194

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shellac

parents:

diff changeset

1195 Workflow authors should provide this in the `hints` section. The

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shellac

parents:

diff changeset

1196 intent of this feature is that workflows produce the same results

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shellac

parents:

diff changeset

1197 whether or not InplaceUpdateRequirement is supported by the

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shellac

parents:

diff changeset

1198 implementation, and this feature is primarily available as an

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shellac

parents:

diff changeset

1199 optimization for particular environments.

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shellac

parents:

diff changeset

1200

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1201 Users and implementers should be aware that workflows that

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1202 destructively modify inputs may not be repeatable or reproducible.

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shellac

parents:

diff changeset

1203 In particular, enabling this feature implies that WorkReuse should

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shellac

parents:

diff changeset

1204 not be enabled.

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shellac

parents:

diff changeset

1205

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parents:

diff changeset

1206 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

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parents:

diff changeset

1207 class:

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parents:

diff changeset

1208 type: string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1209 doc: "Always 'InplaceUpdateRequirement'"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1210 jsonldPredicate:

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parents:

diff changeset

1211 "_id": "@type"

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shellac

parents:

diff changeset

1212 "_type": "@vocab"

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shellac

parents:

diff changeset

1213 inplaceUpdate:

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shellac

parents:

diff changeset

1214 type: boolean

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shellac

parents:

diff changeset

1215

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shellac

parents:

diff changeset

1216 - type: record

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shellac

parents:

diff changeset

1217 name: ToolTimeLimit

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1218 extends: ProcessRequirement

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1219 doc: |

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shellac

parents:

diff changeset

1220 Set an upper limit on the execution time of a CommandLineTool.

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shellac

parents:

diff changeset

1221 A CommandLineTool whose execution duration exceeds the time

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shellac

parents:

diff changeset

1222 limit may be preemptively terminated and considered failed.

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shellac

parents:

diff changeset

1223 May also be used by batch systems to make scheduling decisions.

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shellac

parents:

diff changeset

1224 The execution duration excludes external operations, such as

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1225 staging of files, pulling a docker image etc, and only counts

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1226 wall-time for the execution of the command line itself.

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1227 fields:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1228 - name: class

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1229 type: string

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1230 doc: "Always 'ToolTimeLimit'"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1231 jsonldPredicate:

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1232 "_id": "@type"

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1233 "_type": "@vocab"

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shellac

parents:

diff changeset

1234 - name: timelimit

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shellac

parents:

diff changeset

1235 type: [long, string, Expression]

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1236 doc: |

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1237 The time limit, in seconds. A time limit of zero means no

26e78fe6e8c4 "planemo upload commit c699937486c35866861690329de38ec1a5d9f783"

shellac

parents:

diff changeset

1238 time limit. Negative time limits are an error.

Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/cwltool/schemas/v1.1.0-dev1/CommandLineTool.yml @ 0:26e78fe6e8c4 draft